docs: the handbook follows the three layers: swarm, hives, agents

The handbook's sections were agent-lifecycle, integrations, swarm, tools,
trust-boundary and web-ui, which do not follow how the system is built, so a
reader could not tell which layer a page is about. Its pages now sit in
swarm/, hives/ and agents/, with the accounts an agent can hold outside the
system in external-accounts/.

- swarm/: forge, matrix and the knowledge repo join the swarm pages, and so
  does the swarmctl reference.
- hives/: the dashboard, hivectl and its reference, and the operator/agent
  boundary, with a README that takes over the old web-ui and tools pages.
- agents/: the roster, persistence, config changes, the agent's own web page
  (was web-ui/agent) and the security model, with a README.
- external-accounts/: GitHub and GitLab.

Pages are moved whole; none is split yet. Every reference follows: relative
links in the docs, `docs/2-handbook/...` paths in code comments, the nix
checks that regenerate the CLI references and the ignore list, and docs/README.md,
whose handbook section is now by layer.

nix/host-modules/hive-c0re/default.nix

@@ -181,7 +181,7 @@ in
     # Operators granted sudoless `hivectl`. Members of `hive-admin` can
     # connect to the host admin socket (group-owned by hive-admin via the
     # socket unit's `SocketGroup` below) without root. That socket is *full*
-    # hive control (spawn/kill/destroy/deploy, docs/2-handbook/trust-boundary/boundary.md), so this is
+    # hive control (spawn/kill/destroy/deploy, docs/2-handbook/hives/boundary.md), so this is
     # an explicit opt-in allowlist — empty by default (root-only).
     users.groups.hive-admin = {
       members = controllerCfg.adminUsers;
@@ -362,7 +362,7 @@ in
         # `0660 root:hive-admin` — group-owned by `hive-admin` so operators in
         # that group (services.hyperhive.deploy.hive-controller.adminUsers) drive `hivectl`
         # without root; an empty adminUsers list leaves the group memberless,
-        # so it stays effectively root-only. See docs/2-handbook/trust-boundary/boundary.md.
+        # so it stays effectively root-only. See docs/2-handbook/hives/boundary.md.
         SocketMode = "0660";
         SocketGroup = "hive-admin";
         # Only consulted when the directory is absent at socket-unit

nix/host-modules/hive-c0re/options.nix

@@ -234,7 +234,7 @@ in
         `hivectl` (and thus the whole hive) without `sudo`.
 
         This is a real privilege grant: the admin socket is *full* hive
-        control — spawn / kill / destroy / deploy — see `docs/2-handbook/trust-boundary/boundary.md`.
+        control — spawn / kill / destroy / deploy — see `docs/2-handbook/hives/boundary.md`.
         Keep the list to trusted operators. Empty (the default) keeps the
         socket root-only, as before.
       '';

nix/host-modules/hive-forge/service.nix

@@ -85,7 +85,7 @@ in
 
         Defaults to `https://''${cfg.domain}`, the gateway vhost. When
         `null`, the dashboard **hides** forge links rather than
-        guessing one — see `docs/2-handbook/web-ui/dashboard.md::Container row` for
+        guessing one — see `docs/2-handbook/hives/dashboard.md::Container row` for
         the rationale (a link built from the operator's own browser
         hostname + a container port is only an accident away from
         wrong on any deployment that isn't plain localhost).

nix/host-modules/hive-matrix.nix

@@ -228,7 +228,7 @@ let
   # skips the dart web-worker compile + the emscripten native_imaging
   # build. Two derivations below cover both. Full rationale (why
   # passthru.pubspecLock.dependencySources, why `dontConfigure`, why
-  # `make -C js`, why build-CWD-relative dart path): docs/2-handbook/integrations/matrix.md::
+  # `make -C js`, why build-CWD-relative dart path): docs/2-handbook/swarm/matrix.md::
   # fluffychat-web build fixes.
 
   fluffychat-web-imaging = pkgs.stdenv.mkDerivation {
@@ -312,7 +312,7 @@ in
   # default). Container shape,
   # serverName vs gatewayHost split, provisioning flow (registration
   # token + LoadCredential), assertion rationale, initial rollout
-  # settings: docs/2-handbook/integrations/matrix.md. Vhost map + discovery flow + tuning
+  # settings: docs/2-handbook/swarm/matrix.md. Vhost map + discovery flow + tuning
   # knobs: docs/4-implementation/networking/gateway.md.
 
   # `swarm.matrix`, in ./hive-matrix-service.nix, is what the homeserver IS from
@@ -573,7 +573,7 @@ in
     # hive-network.nix) when not set explicitly, so no separate
     # domain/serverName assertion is needed here. gatewayHost may not be
     # "" (same footgun as forge.domain — nginx rejects an empty
-    # server_name). docs/2-handbook/integrations/matrix.md::Assertion rationale.
+    # server_name). docs/2-handbook/swarm/matrix.md::Assertion rationale.
     assertions = [
       {
         assertion = cfg.gatewayHost == null || cfg.gatewayHost != "";
@@ -765,7 +765,7 @@ in
     # Activation-time token generation — without this the bind-mount
     # would hand tuwunel an empty file on first boot and break every
     # registration until restart. Idempotent;
-    # docs/2-handbook/integrations/matrix.md::Provisioning flow.
+    # docs/2-handbook/swarm/matrix.md::Provisioning flow.
     # Tell an operator whose homeserver already exists that `serverName` is
     # unpinned, at the one moment they are looking: the rebuild.
     #

nix/host-modules/hive-priv.nix

@@ -1,5 +1,5 @@
 # hive-priv — the narrow root privileged helper hive-c0re delegates
-# to, socket-activated at /run/hive/priv.sock. See docs/2-handbook/trust-boundary/boundary.md
+# to, socket-activated at /run/hive/priv.sock. See docs/2-handbook/hives/boundary.md
 # for the operator/agent trust-boundary design.
 {
   pkgs,